Virus-like particle preparation is improved by control over capsomere-DNA interactions during chromatographic purification

Expression of viral capsomeres in bacterial systems and subsequent in vitro assembly into virus-like particles is a possible pathway for affordable future vaccines. However, purification is challenging as viral capsomeres show poor binding to chromatography media. In this study, the behavior of capsomeres in unfractionated bacterial lysate was compared with that for purified capsomeres, with or without added microbial DNA, to better understand reasons for poor bioprocess behavior. We show that aggregates or complexes form through the interaction between viral capsomeres and DNA, especially in bacterial lysates rich in contaminating DNA. The formation of these complexes prevents the target protein capsomeres from accessing the pores of chromatography media. We find that protein-DNA interactions can be modulated by controlling the ionic strength of the buffer and that at elevated ionic strengths the protein-DNA complexes dissociate. Capsomeres thus released show enhanced bind-elute behavior on salt-tolerant chromatography media. DNA could therefore be efficiently removed. We believe this is the first report of the use of an optimized salt concentration that dissociates capsomere-DNA complexes yet enables binding to salt-tolerant media. Post purification, assembly experiments indicate that DNA-protein interactions can play a negative role during in vitro assembly, as DNA-protein complexes could not be assembled into virus-like particles, but formed worm-like structures. This study reveals that the control over DNA-protein interaction is a critical consideration during downstream process development for viral vaccines.

Automated summary

Expression of viral capsomeres in bacterial systems and their subsequent assembly into virus-like particles can be a cost-effective option for future vaccines. However, purification is challenging due to poor binding to chromatography media. This study shows that protein-DNA interactions in bacterial lysates can lead to the formation of complexes that hinder proper purification, but can be modulated by controlling ionic strength to enhance bind-elute behavior on salt-tolerant chromatography media. DNA-protein interactions negatively impact in vitro assembly, forming worm-like structures instead of virus-like particles. Controlling DNA-protein interactions is crucial for downstream viral vaccine process development.